Uber-lawyer David Boise once helped the government split up Microsoft; now he’s helping sink Tyco’s two allegedly crooked ex-honchos, with damaging testimony yesterday in their $600 million embezzlement trial.

Boise, whose firm was hired by Tyco to root out the alleged theft, told Manhattan Supreme Court jurors that in a face-to-face conversation, former CFO Mark Swartz admitted essentially what is now alleged in one of the 11 larceny counts against him – the unauthorized swiping of a $12.5 million bonus in 1999.

Boise said Swartz ‘fessed up after Boise noted that the bonus was not approved by the company board of directors and never reported to the Internal Revenue Service. Prosecutors say ex-CEO Dennis Kozlowski did the same thing with a $25 million bonus that year.

“I told Mr. Swartz that unless there was something I was missing, this was a very serious problem,” Boise told jurors yesterday. “He said it was a mistake and should not have happened,” Boise added of Swartz. The CFO then agreed to pay the money back with interest, Boise recounted.

The admission is damning in two ways for Swartz. It would mean he knew he had done wrong, and it would mean he misinformed jurors when he told them last week that he never said it.

Boise was the last of more than 50 witnesses in the five-month-long case.